The Beginning In The End
by LilBitOBantar
Summary: Sequel to The End In The Beginning. I advise you read that first but your choice. Gene's awake! Can he realise what everyone has been telling him all along before it's too late? The dream was just the beginning and nothing is as it seems...
1. Chapter 1

_Just to stop the confusion, this is still set in 2011. I changed my mind over what year it was going to be so I'm sorry for that. Hope you enjoy the first chapter of my sequel. Please review! :D Btw, the name Alexandra does actually mean 'Protector of Mankind' in Greek. And I got the tarro card meanings online so if they're wrong I'm sorry. :(_

The Beginning in the End

Chapter 1

It had been 3 months since Gene had woken up in the hospital. 3 months since Alex had taken off to France to help out with a case over there. He'd never tell anyone, but he missed her. That coma dream had felt so real to him and he knew that things had changed. But he was too stubborn to admit it. And now sitting here, listening to another bloody doctor, he scowled at the thought of anyone noticing. Dr Jack Storm, the psychiatrist sat opposite him.

"So, Mr Hunt. How are we feeling today?"

"Great, just wonderful! It's been 3 months since they put my brain box through the blender and now I'm back!" He grinned, in spite of himself. Jack raised an eyebrow and looked back down at his paper.

"So the confusion is gone then?"

"Excuse me?" Said Gene puzzled.

"Your memory is completely returned? You're not having anymore strange dreams? Feelings that aren't yours? Seeing things?" Jack said smugly.

"I am just fine, thank you very bloody much!" Gene muttered back irritably.

"Now then Mr Hunt, if that is the case then, do you feel better now they're gone? Or do you miss them? Do you miss anything about them?"

"Oh yeah definitely!" He said enthusiastically. When Jack wrote this down he nodded at him to continue.

"The clothes." Said Gene. "I miss the clothes, and that's about it." _Liar!_ His brain said accusingly, and he frowned angrily at the thought. Jack noticed this and stared at him curiously.

"Why the frown?" He asked. Gene narrowed his eyes at him, confused.

"What are you on about?"

"Why did you frown just now, when I was talking to you about your brain tumour?"

"Probably because I have to listen to all the crap that dribbles out of your gob!" Gene growled back. Jack smiled tentatively at him.

"Mr Hunt, you have been trying to intimidate me from the second you came into the room. You think you can bully your way back onto the job because you're the big man and you always get what you want."

_Not always… _Gene's mind thought. Jack continued,

"You think all this and you've been incredibly annoying. But you're forgetting one very important thing."

"What, that you borrowed your daddy's suit to piss me off in?"

"No. That I'm the one who gets to sign the forms that decide whether or not you are fit for duty." Jack said, simply. Gene's mouth fell open in shock.

"You what?" He cried out angrily. Jack smiled patiently back.

"Yes, Mr Hunt. So I could very easily tell the Governor that your still… How did they put it again? Ah yes, brain damaged." Gene stood up angrily and pointed his finger at Jack.

"Now listen here you psycho-babble-bullshitter," He growled angrily. "I am not brain damaged! I'm not still in dolly dream land, I don't think I'm married to Bolly, I don't own a club, I don't have a daughter and I'm not mega rich! Does this prove I'm not still brain dead?" Jack rolled his eyes and pointed at the sofa across from himself.

"Mr Hunt, please sit down." He said sternly, normally he was a patient guy, but this man was severely testing his limits. Surprisingly Gene sat down and placed his head in his hands.

"It's just so damn confusing. I was in a coma; I had a dream that felt so real that I thought it was reality! I felt things, said things, did things that I haven't in a long time! It changed me, deeply Jack. I still dream about it, about what it was like. And sometimes I almost wish that I could go back there. Things were so much simpler! And my life was basically perfect and I liked it. But now I'm back! I am the Manc Lion! The Guv! I just wanna dive back in, so will you sign the poncy bits o' paper already?" Finishing with a grin, Gene rubbed his hands together and looked back up at Jack; and was surprised to see him smiling. "What?" He asked.

"I'm glad you finally fessed up to what your brain has being yelling at me for the last," Jack looked at his watch. "Hour and a half we have been sitting here. So in that sense, I now pronounce you… Fit for duty!" Reaching under his chair, Jack pulled out Gene's gun and badge and threw them to him. He caught them and narrowed his eyebrows at Jack.

"I can go now right?" He asked suspiciously. Jack nodded.

"Yes you may, but you and Ms Drake will be having weekly therapy with me until further notice. See you in a week." Then stood up and opened the door to his office, gesturing for Gene to leave. But Gene wouldn't budge.

"Hang on a second! Why is Bolly having bloody psycho babble therapy too? She doesn't need any counselling, she could probably talk herself to death already!" He said angrily. Jack laughed.

"I am well aware that Alex is a psychologist. However the counselling is for the both of you as an evaluation after what happened last year." He said, still gesturing towards the door. Gene winced; he hated being reminded of that. The only operation that they had ever failed and it had been their biggest downfall yet. It had torn the team apart for a while, but things were better now, the boys and he were back on good terms and he and Alex were back to their flirty banter and 'eye sex' as Ray so crassly called it. He liked Molly a lot and heard about how her and Nick had been getting to know each other over the summer, whilst Alex was away in France. He wondered when she would be back; she had been gone the whole summer, just like he had except he had been in hospital for most of it and off duty for the rest. He actually missed her. Thinking about ways he could tell her he was back on the job, when she returned; Gene stood up, clapped Jack on the shoulder and walked out his office. Jack watched him round the corner and walk into the lift, doors sliding shut behind him. Then turned back into his office and sat down with a sigh. _This is going to be difficult. _He thought to himself.

**XXXXXXXX**

Alex sighed. She had only just got off the plane from Paris 2 hours ago and she had been sitting at this stupid park picnic-table with Shaz and Avalon – Shaz's 'psychic' – for most of that time. She didn't believe in psychics, not at all. _Ha ha, that's funny!_ She thought, _If Gene were here he would say, "Well, well, well Bolly, for all your psycho-babble-bullshit and you don't believe in the real psychos?" _She sighed inwardly at this. Gene. God how she had missed that man when she went away. She remembered telling him she was going away while he was in the hospital. She remembered the lost look on his face, and even though he wasn't to sure who she was at the time, he had asked her not to leave him. She almost regretted what she had said to him next, tears coming to her eyes as her mind reeled back to that morning.

_Alex walked down the corridor of the hospital, a cardboard container of tea in each hand. She saw Gene laying in his hospital room and, laughing quietly as she saw him talking to the ceiling. Then she knocked gently and pushed the door open with her hip. He looked at her as she came in and almost jumped a mile, scrabbling into a sitting position, as he tried to look normal as possible, in his current situation. Finally he stopped fussing and looked back up at her. _

"_Hello Bolls." He said smiling, Alex was rather dismayed as he seemed generally happy to see her; after all she had only come to give him her news, but she put on a happy front all the same._

"_You remembered my name?" She said smiling back and handed him his tea._

"_I'm wounded Bolly; you think I don't know your name after all our lovely chats and cups of tea?" He said with a signature pout, taking a gulp of his tea and giving an 'Ah' of approval. She laughed at him and smacked him playfully on his arm, taking a sip of her tea and nodding her approval. _

"_Well aren't you glad I went and got you a cuppa from Starbucks? Otherwise we would be drinking the hospital tea and you know what that's like." She said wistfully, raising her eyebrows and smiling cheekily. _

"_Yeah your right, that stuff normally tastes like horse shit!" He laughed back, smiling in spite of himself. She smiled back but he could see that her's was a sad smile, even though she tried her best to hide it._

"_So what's on the agenda today Bolls? More photos or are you gonna tell me some kinky stories of yours?" He said with a smirk and wink, but they disappeared quickly as she looked up, her eyes shining. "Hey, Alex what's up? What's wrong?" She shook her head at him smiling quickly back, but it looked more like a grimace._

"_Uh nothing Gene, absolutely nothing." She replied with a falsely bright air about her. "It's just that I can't really stick around today."_

"_Oh," He said, his mood dampening slightly. "Well will you be back tomorrow?" Alex didn't know why but something in the way he said those words and the look in his eyes made her think that he desperately wanted her to stay, but she brushed it off as guilt. _

"_No, I'm sorry Gene."_

"_Why not?" He sounded like a lost child, it made her feel so sad inside._

_I actually have to go to France to help with a case. Apparently I'm the best for the job so our Super has transferred me for a while." _

"_How long?" _

"_Well… The rest of the summer." She said hesitantly. And she felt her stomach tighten as she saw his face fall, the bright mood crumbling into dust. _

"_Oh. Wow, that's erm, wow." Was that all he could think to say?_

"_I know, but I have to go. The super says I have to and I have to leave Molly with Ray and Maya. But I think her and Nick are getting along quite well so… yeah." _

"_Do you really? Why can't you just stay here? I only really know you out of all the people you introduced me to. And now you're going away? For 3 months!"_

"_I'm sorry." She looked down and so did he, both of them sighing in defeat._

_Gene looked up at her and flashed a fake smile her way. Clapping his hands and rubbing them together he said in a business like tone. "Well Bolly, I hope you have fun and be sure to show us your tan when you get back." She felt a flicker of hurt run across her face but then, shaking her head slightly as if to clear the thoughts from it, Alex stood up._

"_Well then Guv, see you in the fall." She said holding her hand out. He took it gently and held it in between his own._

"_See you in the fall Bolly." And with that she took her hand from his grasp and walked out of the hospital room, pulling a wheelie suitcase behind her and a holdall on her left shoulder. He watched her as her heels clicked down the corridor, the sound getting further and further away as she turned the corner and disappeared. _

As Alex zoomed back out of memory land, she felt a tear drip down her face; quickly she wiped it away and looked back across at Shaz and Avalon, who had just finished placing her cards on the table.

"You ready?" Said Shaz excitedly, almost bouncing in her seat.

"Let's just get this over with." Sighed Alex, her head lolling back in defeat as she waited for her 'reading'. With a nod, Avalon turned over the first card.

"Protector." She said slowly, as she looked at the card carefully. Shaz almost squealed in delight.

"See I told you!" She said excitedly, "The first card is literally your name." Alex rolled her eyes at her and Avalon turned over the second card.

"Ah, the lion's heart." She said with a smile.

"What now?" Said Alex, puzzled.

"I see a man with a lion's heart. He is close to you." Shaz gasped dramatically at this.

"She means the Guv, Alex!" She said, practically hyperventilating.

"What? Gene isn't close to me!" She replied defensively. But Avalon only laughed.

"You and this man have a very deep connection. You are inextricably linked." As she turned over the next card she continued. "This man was lost in a dream world; you brought him the light that showed him the way back."

"The Guv was in a coma!" Chipped in Shaz, "Alex talked to him everyday and he eventually woke up." Alex glared at Shaz.

"So what? The doctor told me that Gene would eventually wake up so it was just potluck that it happened to be the day I was talking to him!" Sighing, Alex flopped her head back in her hands and growled softly, "So can I go now?" Avalon shook her head.

"You've still got one more card." As she flipped it over, it revealed 'death'.

"Well that doesn't look to promising." Smirked Alex sarcastically.

"Your life is heading for a change. The man whose life you saved will strengthen the bond between you." Avalon nodded simply, as if this was normal. Alex mouthed 'Wha?" over at Shaz who shrugged, grinning like a kid at Christmas.

"Look, Ms Harmonia," She said, trying desperately to be patient. "I've just had a long flight and I would like to go home and change."

"Hold your horses Missy!" Said Avalon; reaching over to turn over the next card. But that was the last straw for Alex.

"Right," She said, finally losing her temper. "Thank you very much Ms Harmonia but I really don't believe in psychics." Standing up, she reached for wheelie suitcase and pulled her holdall onto her shoulder. She had just started walking away when Avalon voice made her jump.

"Were you pregnant?" Alex turned sharply around.

"What?" She said. But Shaz butted in.

"Ohmigosh!" She screeched in one big blur. "Yes that's totally right! Sweetie! You were pregnant in the Guv's coma dream!" Alex gave Shaz the death glare and immediately cooled it.

"Trust me Alexandra. You and this man are connected." Said Avalon, and picked up her cards, packing them away slowly. As she picked up the last card, Alex saw it said 'Love'.

Scoffing quietly to herself, she waved goodbye and muttered darkly to herself "Yeah I'll show you a connection. Bloody Shaz! You are so dead." And she carried on walking down the path. Her heels clicking as she went.

**XXXXXXX**

_So what did you think? Please don't kill me. I promise we will have Gene and Alex interaction in the next chapter. I just needed to introduce the new characters and give a little explanation. Please leave a review xx :D_


	2. Chapter 2

_Hey there guys, sorry for the hold up ideas and life being what they are kind of explain an awful lot but I'm back, and they'll be a lot more from me to come. :] Right as I am still sticking to the A2A main plan just a few notes:_

_Sam, Annie, Mac and Gil Hollis will not be in this story - as they are all dead but imagine season 3 never happened and sam and annie died in a car crash. My new characters are based off of previously owned ones, and my narrator is sadly eviserated with Gene's coma world. There may still be a few twists and turns but if you have any suggestions or note please feel free to share them :)_

_As for copyright yadi yada, you all know as well as I do the only things we own are our imaginations and passion for the show, so if anyone wishes to sue me feel free! But I'm English, so I shall just sip my cup of tea and watch it get thrown out of court. :D _

_Now enough of my ramblings! On with the story!_

_Enjoy! (:_

Chapter 2

As Alex entered the station, she saw Chris and Ray heading her way. As their eyes finally connected with her face, registering her presence, they sported grins as bright at bonfire night.

"Boss- I mean, Ma'am!" Chris cried delightedly and ran to hug her. As she was engulfed by Chris' arms, she saw Ray shake his head and mutter 'Poof'. As Chris pulled back, Ray moved forward to pat her on the back.

"-Ey up Alex, we've bloody missed you. Although considering the Guv and your absences, I've done pretty well, holding down the fort." Ignoring his blatant attempt at blowing his own trumpet - _mind out of the gutter Alex_ – she pulled him into a warm hug. Then, pulling away from them both, Alex set off down the corridor laughing quietly to herself as she heard Chris and Ray bickering over who did a better job. As she passed Viv, she slowed her pace slightly moving next to the desk.

"Hello Viv." She said cheerily. He jumped a mile.

"Bugger me sideways!" The elderly Chinese woman standing opposite him at the desk hit him with her handbag, causing Viv to yelp and Alex to giggle.

"Nice to see you too, if anyone needs me I'll be in my office 'de-jet lagging'." Alex smiled, turned and set back down the hall. The click of her heels feeling so familiar to her, the smell of paperwork, metal and cigarette smoke, swirling in her brain, giving her the feeling of home.

As she finally reached her office, she kicked of her shoes, threw her coat and bags messily to the floor and bumped her hip against the bubbly glass door, sliding it shut. Then she dragged her stocking clad feet along the floor until they reached the sofa a little in front of her desk. Unceremoniously she flopped her herself onto it, preparing herself for a good old nap while she passed the sick feeling she always got after travelling so long. At least that's what would've happened, if – when she flopped – she hadn't sat upon a warm and firm unidentified object, which let out a deep yell of surprise, making her jump a mile in the air.

"Jesus!" She yelled. "What the- Gene!" As she turned to confront whoever had ruined her cool down, she saw him climbing to his feet, grinning at her. He looked a mess.

"Christ, Gene why do you look like a furniture mover?" He laughed at her.

"Bolly, you don't see me for 3 months and that's the first question you ask me in the middle of our – soon to be – reunion?" At this, Alex gestured to his low apparel. His hair was mussed; a blonde longish mess atop his head, and the beard growing around his face was definitely not a 5'oclock shadow. Looking further, he was wearing a navy cotton t-shirt with some manly stamp across it, a pair of faded dark jeans and black trainers. Gene looked down to where her hand was.

"Oh, well I only got reinstated today so- Hey! What are the odds of that? Me getting reinstated on the day you come home! That's great Bollykecks." He was grinning like a Cheshire cat now and pulled her into a warm bear hug before she could answer him. Alex smiled into his shoulder, relieved that he was here with her, that they were back! Over her shoulder Gene was grinning, eyes glowing and happy. _Blimey!_ He thought. _I feel all this joy from a hug? I can't wait for the rest! No, no, no Genie boy! Mustn't think all this again, that was just the tumour nothing else._ He was so deep in thought he hadn't realised he was semi crushing Alex as his hold tightened subconsciously at the thought of them; Alex began to squirm, trying to get some space between them and some air back into her body.

"Gene? GENE! God I missed you but you're going to kill me if I am deprived of anymore oxygen- LET GO!" Hearing her yell at him he jumped back in shock, eyes bugging slightly.

"Lord, sorry Bolly its just been that long since someone hugged me! I mean 3 months I'm going stir crazy!" He was running his hands through his hair as he babbled, making it look more rugged and wild. She smiled at him, silently taking note that he looked so much younger, freer. He smiled back, and together, in that moment, they felt the whole world blacken around them – like they were the only people left in the world. Just as they drew closer to each other-

BANG!

The door of Alex's office shot open, causing the two to fly apart and glare angrily at the intruder. Shaz stared wide eyed back at them.

"Sorry guys I just needed to s…" She stopped mid sentence. "Oh my god Mr 'Unt you're back! Sorry to intrude but Avalon just told me that there are a load of dead bodies buried under Fenchurch park fountain!"

"Who the hell's Avalon?" Said Gene puzzled, Alex rolled her eyes and looked over at his.

"Avalon is Shaz's 'psychic'." She explained using her air quotes, at this Gene scoffed and blew a loud raspberry.

"See Shaz, even superstitious Hunt doesn't believe in psychics!" Shaz sent a smug grin their way.

"Oh really, well she also told me that the two of you are linked in a very profound manor, and that Ma'am was pregnant in your coma dream Guv." Gene paled at this and looked over at Alex. She grinned at him and blew a loud raspberry like he had moments ago, which Gene joined in – if only to cover up his blunder.

"Fine, fine," Shaz grinned. "Say what you will but please, please just go and check it out. Because I will never set foot in that park again if I'm not totally certain that there are none and I have to imagine dead people buried under it as I walk!" She seemed a little hysterical now, so Gene nodded hurriedly and ushered her out of the office, closing the door behind her. He then turned back to Alex and sighed smiling, running a hand over his face. Then his head snapped up.

"Let's go!" He cried excitedly. Alex looked puzzlingly back at him.

"What? You don't believe her story do you?"

"Of course not but it's been 3 months Bolly, 3 Months of nothing but scotch and bullshit therapy I need to get out!" His puppy pout made her raised eyebrow falter a little, and Alex sighed in defeat.

"Fine, fine but can I at least shower first!"

"Hmm," Gene rumbled. "I really need a shave." Alex scoffed at this and walked into her office bathroom. Gene heard the door slam and waited till he heard the shower water running to let out the breath he had been holding in as soon as those delicious hips of hers began to sway once more. It was ironic really, from his past brain damage she was the one constant thing he remembered above all others, but she was also the thing he was trying desperately not to think about. _Huh, isn't that just a Bitch._

Stepping quietly out of her office and closing the door behind him, he set off down the hall, thoughts wandering back to what Shaz had said about their 'profound link'. He really needed to talk with this psychic; maybe she could give him a couple of those magical juju answers to his big question.

**XXXXXXXX**

Down the hall a commotion sounded, men's voices yelling, women screaming, papers and utensils flying everywhere. In the midst of the fray a tall, dark man stepped from the crowd, he stopped taking a puff of his cigarette, glasses glinting in the reflection of the lighting panels above. His crooked smile matched his deep black eyes, like bottomless pits of darkness. Observing the chaos surrounding him, he closed his eyes – smile still firmly in place – and let out a small chuckle.

"Oh I think I'm gonna like it 'ere. Yes, I think it will do nicely." The man then strode off down the building towards the stairs, checking for the floor to C.I.D

**XXXXXXXX**

_Right ooh bit of a mysterious bloke at the end, wonder how many of you will guess the identity correctly ;) He he, sorry for the shortness but the next chapter will be all one big Galexy block, this was more of a run up for the big revelation where we will see an insightful Ray! Yay :D_

_Please review if you're still with me!_

xoxo


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